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[OBG] Nature of Race Full

(2015-Apr-19, 00:55:36)Chuck Wrote: I will make public the list of reviewer requests I have sent out. I am primarily emailing researchers who have written about the biological concept.

(1) Adam Hochman -- kindly notified me that he had other commitments (received 4/18)

(2) Michael O. Hardimon -- pending (sent 4/14)

(3) Jeremy Pierce -- No reply (sent 4/08)

(4) Michael Levin -- Accepted, then no reply after (sent 3/13)

(5) Michael Woodley -- Replied, noted he liked it, but said to publish elsewhere (sent 3/13)

(6) Neven Sesardic -- Replied, busy (3/11)


(7) Philosopher Michael James (who wrote the Stanford article on race)-- Politely declined (4/21)

(8) After initially accepting (4/20), Robin Andreasen politely reneged (4/30).

(9) I didn't direly ask Johnathan Kaplan because he told one of my reviewers (3/20) that he didn't want to engage with "racists, nor people who spout racist nonsense while hiding behind mealy-mouthed denials", that the reviewer should have fun hanging out with other racists on websites like ODP/OBG and engaging in "terribly projects", and that I was a
"intellectually dishonest racist". I presumed, based on this, that he would refuse a review request.

(10) Justine Smith -- politely declined (5/1)

(11) Joshua Glasgow -- politely declined (5/1)

(12) Kenan Malik -- politely declined (5/3)
[/quote]

(13) Quayshawn Spencer -- politely declined, busy (5/4)

(14) Matthew Kopec -- politely declined, was hesitant given the journal's unestablished reputation (and hereditarian leaning) (5/4)

(15) Koffi Maglo -- politely declined (5/4)

(16) Roberta Millstein -- politely decline (5/5)
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(2015-May-04, 19:58:20)Duxide Wrote: This is a very long paper. I think a lot of people are discouraged by its sheer size. Perhaps crowdfund it and make a payment to the reviewer conditional on receiving a review (no matter whether it's positive or negative).I could act as intermediary.


Davide,

I am trying to get the paper reviewed by someone who is actually somewhat familiar with the topic. When that fails -- that is, when I exhaust my twoscore long list of those who have recently written on the race concept (as such) -- I will insist that someone on the OBG editorial board review it, which will possibly mean you. As you reviewed John Harvey's book on race and as you conduct pop. genetic research you are at least qualified to review my paper. If it comes to that, I would be happy to compensate you or whomever for time spent. Maybe 100 Euros or so, since this is what paid reviewers get; there would, of course, be no expectation that you would approve.
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I'm fairly familiar with the philosophy of science, population genetics as well as of course the differential psychological/sociological literature, but since we coauthor so often, I'm not really an independent, neutral reviewer.
 Reply
(2015-May-05, 17:53:59)Emil Wrote: I'm fairly familiar with the philosophy of science, population genetics as well as of course the differential psychological/sociological literature, but since we coauthor so often, I'm not really an independent, neutral reviewer.


You can always give an informal critique.
 Reply
I believe I have written several long comments already. :)
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Chuck,

Is there any point in looking for new reviewers? The subject itself is controversial and some criticisms will be motivated by blind hostility. If you look hard enough you may find a prestigious reviewer who is willing to review. But is it worth the trouble? Even if the reviewer is fair and impartial, he or she will focus on certain minor details (because of the sheer length of the text).

It may be useful to have some kind of preface that could orient the reader. What general questions are you trying to resolve? What are the obstacles to resolving them?

Where can I find the latest version of your text?
 Reply
(2015-May-05, 20:15:03)Peter Frost Wrote: Chuck,

Is there any point in looking for new reviewers? The subject itself is controversial and some criticisms will be motivated by blind hostility. If you look hard enough you may find a prestigious reviewer who is willing to review. But is it worth the trouble? Even if the reviewer is fair and impartial, he or she will focus on certain minor details (because of the sheer length of the text).

It may be useful to have some kind of preface that could orient the reader. What general questions are you trying to resolve? What are the obstacles to resolving them?

Where can I find the latest version of your text?



Peter,

The latest version is here: https://osf.io/2wsuh/ Some of the formatting screwed up because I switched to word 2007. I added a more detailed abstract, which summarizes the main points and some more discussion in defense of one of my main points -- i.e., early subspecies concepts = genealogically understood constant varieties.

As for this question, "Is there any point in looking for new reviewers?", I was hoping to get confirmation concerning some of the points and clarification concerning some of the arguments which I critiqued -- thus I have been emailing mostly those whom I have critiqued.

As for, "It may be useful to have some kind of preface that could orient the reader. What general questions are you trying to resolve? What are the obstacles to resolving them?"

I think the abstract now makes this clear. Though, I could elaborate more, I guess.


I'm stuck on this question, though -- which I can't seem to get an answer to:

............................................................................

Dear Blah blah blah

I am writing to see if either of you could help with a population genetic question, a clear answer to which has been eluding me.

For context, I am writing a paper on the biological race concept in relations to our species.

I would like to determine, based on genetic differentiation values (e.g., SNP Fst values), what the expected between-group-variance would be for an average quantitative trait owing to neutral divergence.

Would it be:

(a) ~Fst (treating this as an F-ratio that could be converted into mean standardized differences)
(b) ~2*Fst ("")
© Something else.

Much of the literature discusses the matter in terms of Qst, defining this as GB/(GB + 2GW). And Qst is said to come out to Fst.

But it's not clear to me if, for diploids (where roughly half of the genetic variance is trapped within individual), the expected quantitative trait F-ratio would be equal to 1* or to 2* Fst.

I stumbled across this discussion by Whitlock (2008) ( "Evolutionary inference from QST")

"Does FST = QST for neutral traits?

The calculation of QST for a trait requires two quantities: the additive genetic variance of the trait within a population (VA,within) and the genetic variance among populations (VG,among). For diploids, QST is calculated as

Qst = GB/(GB + 2GW)

For haploids, the same equation applies, but without the '2' in the denominator. [That '2' for the diploid case comes from the fact that the quantitative genetic variance among populations is proportional to two times FST (Wright 1951).] "

...

It seems to say that the expected between population quant variance would be 2*Fst.

This strikes me as being rather high, though.

To take human continental natural divisions as an example, the Fst SNP value is ~ 0.12.

This would then given F-ratio = 2*0.12 = 0.24 which would be equivalent to an average d-value > 1.00.

From what I recall the typical phenotypic F-ratio, though, is around 0.10 (i.e., in dental and craniometric traits).

Blah blah blah...

.............................

You wouldn't have any idea, would you? I asked Henry Harpending who is more familiar with the Qst literature (inferences of neutral phenotypic divergence from genetic data), but he wasn't sure. I got the basic idea. But I wasn't able to be precisely clear in my discussion because I couldn't resolve this issue -- so I had to talk around it.

(Ya, I understand your apples to oranges point -- I would still like to know what the predicted quantitative trait variation would be due to neutral divergence. See this paper for context: Leinonen, et al. (2013). QST-FST comparisons: evolutionary and ecological insights from genomic heterogeneity.)
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(2015-May-05, 22:19:30)Chuck Wrote: I'm stuck on this question, though -- which I can't seem to get an answer to:

............................................................................

Dear Blah blah blah

I am writing to see if either of you could help with a population genetic question, a clear answer to which has been eluding me.

For context, I am writing a paper on the biological race concept in relations to our species.

I would like to determine, based on genetic differentiation values (e.g., SNP Fst values), what the expected between-group-variance would be for an average quantitative trait owing to neutral divergence.

Would it be:

(a) ~Fst (treating this as an F-ratio that could be converted into mean standardized differences)
(b) ~2*Fst ("")
© Something else.

Much of the literature discusses the matter in terms of Qst, defining this as GB/(GB + 2GW). And Qst is said to come out to Fst.

But it's not clear to me if, for diploids (where roughly half of the genetic variance is trapped within individual), the expected quantitative trait F-ratio would be equal to 1* or to 2* Fst.

I stumbled across this discussion by Whitlock (2008) ( "Evolutionary inference from QST")

"Does FST = QST for neutral traits?

The calculation of QST for a trait requires two quantities: the additive genetic variance of the trait within a population (VA,within) and the genetic variance among populations (VG,among). For diploids, QST is calculated as

Qst = GB/(GB + 2GW)

For haploids, the same equation applies, but without the '2' in the denominator. [That '2' for the diploid case comes from the fact that the quantitative genetic variance among populations is proportional to two times FST (Wright 1951).] "

...

It seems to say that the expected between population quant variance would be 2*Fst.

This strikes me as being rather high, though.

To take human continental natural divisions as an example, the Fst SNP value is ~ 0.12.

This would then given F-ratio = 2*0.12 = 0.24 which would be equivalent to an average d-value > 1.00.

From what I recall the typical phenotypic F-ratio, though, is around 0.10 (i.e., in dental and craniometric traits).

Blah blah blah...

.............................

You wouldn't have any idea, would you? I asked Henry Harpending who is more familiar with the Qst literature (inferences of neutral phenotypic divergence from genetic data), but he wasn't sure. I got the basic idea. But I wasn't able to be precisely clear in my discussion because I couldn't resolve this issue -- so I had to talk around it.

(Ya, I understand your apples to oranges point -- I would still like to know what the predicted quantitative trait variation would be due to neutral divergence. See this paper for context: Leinonen, et al. (2013). QST-FST comparisons: evolutionary and ecological insights from genomic heterogeneity.)

First of all, the set of 315 Fst values that I calculated using VCFtools (which employs Weir and Cockeram Fst formula) on 1000 Genomes phase 3 data for 26 populations can be seen here (https://docs.google.com/spreadsheets/d/1...sp=sharing ). I report Fst for 1st and 21st chromosomes (columns C and D). They are practically identical (r=0.995) so either can be used to represent the whole genome. Note that these include SNPs and indels. If you use these Fst values in your paper, please cite my last article (http://dx.doi.org/10.6084/m9.figshare.1393160 ) because they are in the supplementary material there.

THERE IS INDEED MUCH CONFUSION ON INTERPRETING FST AS RELATIVE BETWEEN POPULATION VARIANCE.
It appears that the expected BETWEEN population variance should be 2*Fst, after correcting for the inbreeding coefficient.

Sarich and Miele (2004) write "Lewontin had noted that 85% of the genetic variability was among individuals within populations, and only an additional 15% was added when individuals in different populations were compared [...]. The point is that we are diploid organisms, getting one set of chromosomes from one parent and a second from the other. To the extent that your mother and father are not especially closely related, then, those two sets of chromosomes will come close to being a random sample of the chromosomes in your population. And the sets present in some randomly chosen member of yours will also be about as different from your two sets as they are from one another. So how much of the variability will be distributed where?
First is the 15% that is interpopulational. The other 85% will then split half and half (42.5%) between the intra- and interindividual within-population comparisons. The increase in variability in between-population comparisons is thus 15% against the 42.5% that is between individual within-population. Thus, 15/42.5=32.5%... "

So your hunch was right in telling you that Fst underestimates the between-population comparisons by about a factor of 2 (in reality it's a little less than 2 if we account for inbreeding).

Sarich, V. and Miele, F. (2004). Race. The reality of human differences. pp 168-169.
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"I would like to determine, based on genetic differentiation values (e.g., SNP Fst values), what the expected between-group-variance would be for an average quantitative trait owing to neutral divergence."

It would be a bit less than Lewontin's figure of 15%. Selective value varies considerably among genes, with most being close to selective neutrality.

I never really understood the relevance of Henry's criticism of Lewontin's model (i.e., a large chunk of within-group genetic differences are actually within-individual). This criticism would presumably apply to all diploid species, so Fst would have to be adjusted for all diploid species. Yes, between-group variability would look larger for humans, but it would also be proportionately larger for all diploid species.

Fst has acquired an aura of respectability among population geneticists, yet it doesn't tell us half of what we think it does.

I like your abstract. I still disagree with your positive assessment of pre-Darwinian anthropology. Before Darwin, anthropologists had a lot of false premises that prevented them from thinking clearly (young Earth creationism, belief in the flood and Noah's ark, inheritance of acquired characteristics, belief in pre-Adamite races, etc.)
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(2015-May-06, 18:41:23)Peter Frost Wrote: It would be a bit less than Lewontin's figure of 15%. Selective value varies considerably among genes, with most being close to selective neutrality.

I never really understood the relevance of Henry's criticism of Lewontin's model (i.e., a large chunk of within-group genetic differences are actually within-individual). This criticism would presumably apply to all diploid species, so Fst would have to be adjusted for all diploid species. Yes, between-group variability would look larger for humans, but it would also be proportionately larger for all diploid species.



Fst has acquired an aura of respectability among population geneticists, yet it doesn't tell us half of what we think it does.



[Edited for redundant babbling.]

Peter,

I agree with the last point. As for the first, it's a basic quantitative question for which I am receiving conflicting answers. For example, Davide said ~ 2*Fst and you said ~ Fst. Well, both of you can not be correct.

But why does it matter? For one, I just like to get straight answers. For another, it's relevant to the debate since one of the arguments against the significance of major human races is that between group variance is small relative to that between individuals. This is a valid argument since we are often interested in between group to between individual comparisons -- for example, this is typically how we compare differences in the social sciences (e.g., standardized ones). We don't -- I don't at any rate -- typical compare behavioral, morphological, and outcome differences between e.g., Han and Hausa to that between horses and humans, rather we compare it to that between individuals within populations.

Of course, I agree that the precise relation between Fst and quantitative variance, specifically the question I am asking, is irrelevant to intra-species comparisons. I do discuss such comparisons in one of my sections. And I note the difficulties and intricacies with them, especially in regards to measures of divergence. I could have elaborated more and discussed the points which you have made e.g., regarding some obscure deer super-species. But the inter-species stuff doesn't really garner my interest.

Davide,

An equation I have come across for diploids is 2*Fst/(1-Fst) -- which is supposedly derivable from Wright's 1950 equations. See box 1 here. For haploids it is Fst/(1-Fst). I can't make sense of the math, though -- so I want verification from someone who can. (The relation between quantitative trait variance -- i.e., in the sense of F-ratios -- and genetic variance is not directly discussed, rather Qst and Fst is and derivations of Qst are only noted in passing.) I attached some papers on the issue.

It's really a somewhat trivial matter -- I'm just having trouble getting a clear, definitive answer.


Attached Files
.pdf   The genetic differentiation at quantitative trait loci under local adaptation.pdf (Size: 451.29 KB / Downloads: 375)
.pdf   The genetic structure of populationswright1950.pdf (Size: 1.91 MB / Downloads: 721)
.pdf   ComparingFsttoQst.pdf (Size: 587.11 KB / Downloads: 417)
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